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Persistent homology

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https://www.readbyqxmd.com/read/28535128/low-and-high-let-ionizing-radiation-induces-delayed-homologous-recombination-that-persists-for-two-weeks-before-resolving
#1
Christopher P Allen, Hirokazu Hirakawa, Nakako Izumi Nakajima, Sophia Moore, Jingyi Nie, Neelam Sharma, Mayumi Sugiura, Yuko Hoki, Ryoko Araki, Masumi Abe, Ryuichi Okayasu, Akira Fujimori, Jac A Nickoloff
Genome instability is a hallmark of cancer cells and dysregulation or defects in DNA repair pathways cause genome instability and are linked to inherited cancer predisposition syndromes. Ionizing radiation can cause immediate effects such as mutation or cell death, observed within hours or a few days after irradiation. Ionizing radiation also induces delayed effects many cell generations after irradiation. Delayed effects include hypermutation, hyper-homologous recombination, chromosome instability and reduced clonogenic survival (delayed death)...
May 23, 2017: Radiation Research
https://www.readbyqxmd.com/read/28532790/a-safe-and-molecular-tagged-brucella-canis-ghosts-confers-protection-against-virulent-challenge-in-mice
#2
Jing Qian, Zhaoyang Bu, Xulong Lang, Guangmou Yan, Yanling Yang, Xiuran Wang, Xinglong Wang
Canine brucellosis, caused by Brucella canis, is a persistent infectious reproductive disease in dogs. The absence of effective treatment to the intracellular pathogen and the irreversible consequence of infection makes the need of a specific vaccine urgent. Bacterial ghosts (BGs) are the empty envelopes of bacteria with no genome content inside, which emerge as a proper vaccine candidate due to its intact outer antigen. It is generally derived from a genetically engineered strain, through the expression of Bacteriophage phiX174 lysis E gene upon induction...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28528961/gp5-of-porcine-reproductive-and-respiratory-syndrome-virus-prrsv-as-a-target-for-homologous-and-broadly-neutralizing-antibodies
#3
REVIEW
Luca N Popescu, Benjamin R Trible, Nanhua Chen, Raymond R R Rowland
Virus neutralization (VN) responses range from narrowly focused antibodies with only homologous neutralizing activity against the virus used for infection, to antibodies that can neutralize both Type 1 and Type 2 viruses, referred to as broadly neutralizing antibody (bnAb). Even though neutralizing epitopes are likely distributed among several structural glycoproteins, this paper focuses on the ectodomain region of GP5 as a model system for investigating the role for neutralizing and non-neutralizing antibodies in protection and disease...
April 29, 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28526296/mesenchymal-stem-cells-mscs-attenuate-cutaneous-sclerodermatous-graft-versus-host-disease-scl-gvhd-through-inhibition-of-immune-cell-infiltration-in-a-mouse-model
#4
Ji-Young Lim, Da-Bin Ryu, Sung-Eun Lee, Gyeongsin Park, Chang-Ki Min
Human chronic graft-versus-host disease (CGVHD) shares clinical characteristics with a murine sclerodermatous GVHD (Scl-GVHD) model that is characterized by skin thickening and lung fibrosis. A B10.D2 → BALB/c transplant model of Scl-GVHD was used to address the therapeutic effect of mesenchymal stem cells (MSCs) on the development of CGVHD. The clinical and pathological severity of cutaneous Scl-GVHD was significantly attenuated in MSC-treated recipients relative to Scl-GVHD controls. After MSC treatment, skin collagen production was significantly reduced with consistent downregulation of TGF-β expression...
May 16, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28514186/apc-c-cdc20-mediates-deprotection-of-centromeric-cohesin-at-meiosis-ii-in-yeast
#5
Katarzyna Jonak, Ievgeniia Zagoriy, Tugce Oz, Peter Graf, Julie Rojas, Valentina Mengoli, Wolfgang Zachariae
Cells undergoing meiosis produce haploid gametes through one round of DNA replication followed by two rounds of chromosome segregation. This requires that cohesin complexes, which establish sister chromatid cohesion during S phase, are removed in a stepwise manner. At meiosis I, the separase protease triggers the segregation of homologous chromosomes by cleaving cohesin's Rec8 subunit on chromosome arms. Cohesin persists at centromeres because the PP2A phosphatase, recruited by the shugoshin protein, dephosphorylates Rec8 and thereby protects it from cleavage...
May 17, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28498844/windowed-persistent-homology-a-topological-signal-processing-algorithm-applied-to-clinical-obesity-data
#6
Craig Biwer, Amy Rothberg, Heidi IglayReger, Harm Derksen, Charles F Burant, Kayvan Najarian
Overweight and obesity are highly prevalent in the population of the United States, affecting roughly 2/3 of Americans. These diseases, along with their associated conditions, are a major burden on the healthcare industry in terms of both dollars spent and effort expended. Volitional weight loss is attempted by many, but weight regain is common. The ability to predict which patients will lose weight and successfully maintain the loss versus those prone to regain weight would help ease this burden by allowing clinicians the ability to skip treatments likely to be ineffective...
2017: PloS One
https://www.readbyqxmd.com/read/28497794/pore-configuration-landscape-of-granular-crystallization
#7
M Saadatfar, H Takeuchi, V Robins, N Francois, Y Hiraoka
Uncovering grain-scale mechanisms that underlie the disorder-order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology...
May 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/28491250/prevalence-of-hepatitis-c-virus-genotype-3a-in-patients-with-hodgkin-and-non-hodgkin-lymphoma
#8
Hashem Radmehr, Manoochehr Makvandi, Alireza Samarbafzadeh, Ali Teimoori, Niloofar Neisi, Mojtaba Rasti, Sara Abasifar, Hasan Soltani, Samaneh Abbasi, Hadis Kiani, Hamide Mehravaran, Azarakhsh Azaran, Toran Shahani
BACKGROUND AND OBJECTIVES: Hepatitis C virus (HCV) is a major public health problem worldwide. Replication and persistence of HCV genome have been described in the liver tissue as well as B cells lymphocyte. Several investigations have reported that long-term persistence of HCV in B cells may result in Hodgkin and Non-Hodgkin lymphoma. This study was aimed to determine frequency of HCV RNA in histological tissues obtained from patients suffered from Hodgkin and Non-Hodgkin lymphoma. MATERIALS AND METHODS: 52 formalin-fixed paraffin-embedded tissue blocks including 23 (44...
December 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/28472268/nickel-induces-transcriptional-down-regulation-of-dna-repair-pathways-in-tumorigenic-and-non-tumorigenic-lung-cells
#9
Susan E Scanlon, Christine D Scanlon, Denise C Hegan, Parker L Sulkowski, Peter M Glazer
The heavy metal nickel is a known carcinogen, and occupational exposure to nickel compounds has been implicated in human lung and nasal cancers. Unlike many other environmental carcinogens, however, nickel does not directly induce DNA mutagenesis, and the mechanism of nickel-related carcinogenesis remains incompletely understood. Cellular nickel exposure leads to signaling pathway activation, transcriptional changes, and epigenetic remodeling, processes also impacted by hypoxia, which itself promotes tumor growth without causing direct DNA damage...
May 2, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28471170/resveratrol-reactivates-latent-hiv-through-increasing-histone-acetylation-and-activating-heat-shock-factor-1
#10
Xiaoyun Zeng, Xiaoyan Pan, Xinfeng Xu, Jian Lin, Fuchang Que, Yuanxin Tian, Lin Li, Shuwen Liu
The persistence of latent HIV reservoirs presents a significant challenge to viral eradication. Effective latency reversing agents (LRAs) based on "shock and kill" strategy are urgently needed. The natural phytoalexin resveratrol has been demonstrated to enhance HIV gene expression, although its mechanism remains unclear. In this study, we demonstrated that resveratrol was able to reactivate latent HIV without global T cell activation in vitro. Mode of action studies showed resveratrol-mediated reactivation from latency did not involve the activation of silent mating type information regulation 2 homologue 1 (SIRT1), which belonged to class-3 histone deacetylase (HDAC)...
May 23, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28456167/persistent-homology-of-time-dependent-functional-networks-constructed-from-coupled-time-series
#11
Bernadette J Stolz, Heather A Harrington, Mason A Porter
We use topological data analysis to study "functional networks" that we construct from time-series data from both experimental and synthetic sources. We use persistent homology with a weight rank clique filtration to gain insights into these functional networks, and we use persistence landscapes to interpret our results. Our first example uses time-series output from networks of coupled Kuramoto oscillators. Our second example consists of biological data in the form of functional magnetic resonance imaging data that were acquired from human subjects during a simple motor-learning task in which subjects were monitored for three days during a five-day period...
April 2017: Chaos
https://www.readbyqxmd.com/read/28451945/herpesviral-capture-of-immunomodulatory-host-genes
#12
REVIEW
Günther Schönrich, Mohammed O Abdelaziz, Martin J Raftery
Herpesviruses have acquired numerous genes from their hosts. Although these homologs are not essential for viral replication, they often have important immunomodulatory functions that ensure viral persistence in the host. Some of these viral molecules are called virokines as they mimic cellular cytokines of their host such as interleukin-10 (cIL-10). In recent years, many viral homologs of IL-10 (vIL-10s) have been discovered in the genome of members of the order Herpesvirales. For some, gene and protein structure as well as biological activity and potential use in the clinical context have been explored...
April 27, 2017: Virus Genes
https://www.readbyqxmd.com/read/28451879/dynamical-persistence-of-active-sites-identified-in-maltose-binding-protein
#13
Dragan Nikolić, Violeta Kovačev-Nikolić
This study identifies dynamical properties of maltose-binding protein (MBP) useful in unveiling active site residues susceptible to ligand binding. The described methodology has been previously used in support of novel topological techniques of persistent homology and statistical inference in complex, multi-scale, high-dimensional data often encountered in computational biophysics. Here we outline a computational protocol that is based on the anisotropic elastic network models of 14 all-atom three-dimensional protein structures...
May 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28441305/step-by-step-technique-for-segmental-reconstruction-of-reverse-hill-sachs-lesions-using-homologous-osteochondral-allograft
#14
Hassanin Alkaduhimi, Michel P J van den Bekerom, Derek F P van Deurzen
Posterior shoulder dislocations are accompanied by high forces and can result in an anteromedial humeral head impression fracture called a reverse Hill-Sachs lesion. This reverse Hill-Sachs lesion can result in serious complications including posttraumatic osteoarthritis, posterior dislocations, osteonecrosis, persistent joint stiffness, and loss of shoulder function. Treatment is challenging and depends on the amount of bone loss. Several techniques have been reported to describe the surgical treatment of lesions larger than 20%...
June 2017: Techniques in Hand & Upper Extremity Surgery
https://www.readbyqxmd.com/read/28418852/structural-homologies-between-phenformin-lipitor-and-gleevec-aim-the-same-metabolic-oncotarget-in-leukemia-and-melanoma
#15
REVIEW
Gábor Somlyai, T Que Collins, Emmanuelle J Meuillet, Patel Hitendra, Dominic P D'Agostino, László G Boros
Phenformin's recently demonstrated efficacy in melanoma and Gleevec's demonstrated anti-proliferative action in chronic myeloid leukemia may lie within these drugs' significant pharmacokinetics, pharmacodynamics and structural homologies, which are reviewed herein. Gleevec's success in turning a fatal leukemia into a manageable chronic disease has been trumpeted in medical, economic, political and social circles because it is considered the first successful targeted therapy. Investments have been immense in omics analyses and while in some cases they greatly helped the management of patients, in others targeted therapies failed to achieve clinically stable recurrence-free disease course or to substantially extend survival...
March 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28415283/quantifying-disorder-in-colloidal-films-spin-coated-onto-patterned-substrates
#16
Raheema Aslam, Sergio Ardanza-Trevijano, Kristin M Poduska, Anand Yethiraj, Wenceslao González-Viñas
Polycrystals of thin colloidal deposits, with thickness controlled by spin-coating speed, exhibit axial symmetry with local 4-fold and 6-fold symmetric structures, termed orientationally correlated polycrystals (OCPs). While spin-coating is a very facile technique for producing large-area colloidal deposits, the axial symmetry prevents us from achieving true long-range order. To obtain true long-range order, we break this axial symmetry by introducing a patterned surface topography and thus eliminate the OCP character...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28411218/the-conjugative-relaxase-trwc-promotes-integration-of-foreign-dna-in-the-human-genome
#17
Coral González-Prieto, Richard Gabriel, Christoph Dehio, Manfred Schmidt, Matxalen Llosa
Bacterial conjugation is a mechanism of horizontal DNA transfer. The relaxase TrwC of the conjugative plasmid R388 cleaves one strand of the transferred DNA at the oriT, covalently attaches to it and leads the ssDNA into the recipient cell. In addition, TrwC catalyzes site-specific integration of the transferred DNA into its target sequence present in the genome of the recipient bacterium. Here, we report the analysis of the efficiency and specificity of the integrase activity of TrwC in human cells, using the Type IV Secretion System of the human pathogen Bartonella henselae to introduce relaxase-DNA complexes...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28405385/cranial-arterial-patterns-of-the-alpaca-camelidae-vicugna-pacos
#18
Haley D O'Brien
Artiodactyl cranial arterial patterns deviate significantly from the standard mammalian pattern, most notably in the possession of a structure called the carotid rete (CR)-a subdural arterial meshwork that is housed within the cavernous venous sinus, replacing the internal carotid artery (ICA). This relationship between the CR and the cavernous sinus facilitates a suite of unique physiologies, including selective brain cooling. The CR has been studied in a number of artiodactyls; however, to my knowledge, only a single study to date documents a subset of the cranial arteries of New World camelids (llamas, alpacas, vicugñas and guanacoes)...
March 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28402879/fragment-based-nmr-study-of-the-conformational-dynamics-in-the-bhlh-transcription-factor-ascl1
#19
Lorenzo Baronti, Tomáš Hošek, Sergio Gil-Caballero, Hadas Raveh-Amit, Eduardo O Calçada, Isabel Ayala, András Dinnyés, Isabella C Felli, Roberta Pierattelli, Bernhard Brutscher
The Achaete-scute homolog 1 (Ascl1) protein regulates a large subset of genes that leads neuronal progenitor cells to distinctive differentiation pathways during human brain development. Although it is well known that Ascl1 binds DNA as a homo- or heterodimer via its basic helix-loop-helix (bHLH) motif, little is known about the conformational sampling properties of the DNA-free full-length protein, and in particular about the bHLH domain-flanking N- and C-terminal segments, which are predicted to be highly disordered in solution...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28394908/natural-non-homologous-recombination-led-to-the-emergence-of-a-duplicated-v3-ns5a-region-in-hcv-1b-strains-associated-with-hepatocellular-carcinoma
#20
Hélène Le Guillou-Guillemette, Adeline Pivert, Elise Bouthry, Cécile Henquell, Odile Petsaris, Alexandra Ducancelle, Pascal Veillon, Sophie Vallet, Sophie Alain, Vincent Thibault, Florence Abravanel, Arielle A Rosenberg, Elisabeth André-Garnier, Jean-Baptiste Bour, Yazid Baazia, Pascale Trimoulet, Patrice André, Catherine Gaudy-Graffin, Dominique Bettinger, Sylvie Larrat, Anne Signori-Schmuck, Hénia Saoudin, Bruno Pozzetto, Gisèle Lagathu, Sophie Minjolle-Cha, Françoise Stoll-Keller, Jean-Michel Pawlotsky, Jacques Izopet, Christopher Payan, Françoise Lunel-Fabiani, Christophe Lemaire
BACKGROUND: The emergence of new strains in RNA viruses is mainly due to mutations or intra and inter-genotype homologous recombination. Non-homologous recombinations may be deleterious and are rarely detected. In previous studies, we identified HCV-1b strains bearing two tandemly repeated V3 regions in the NS5A gene without ORF disruption. This polymorphism may be associated with an unfavorable course of liver disease and possibly involved in liver carcinogenesis. Here we aimed at characterizing the origin of these mutant strains and identifying the evolutionary mechanism on which the V3 duplication relies...
2017: PloS One
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